Photonic crystals are extremely sensitive to structural disorder even to the point of completely losing their functionalities. While, on one side, this can be detrimental for applications in traditional optical devices, on the other side, it gives also rise to very interesting new physics and maybe even new applications. We propose a route to introduce disorder in photonic crystals in a controlled way by creating a certain percentage of vacancies in the lattice. We show how the method works and what type of materials can be obtained this way. Also, we use this system to probe the role of disorder on the resulting transport properties from various points of view, including measurements of the transport and scattering mean free path and the diffusion constant.